Papers by Dmitrij Rappoport
Photoinduced Intramolecular Charge Transfer in 4-(Dimethyl)aminobenzonitrile − A Theoretical Perspective
Journal of the American Chemical Society, Jan 7, 2004
Recent advances in time-dependent density functional theory (TDDFT) have led to computational met... more Recent advances in time-dependent density functional theory (TDDFT) have led to computational methods that can predict properties of photoexcited molecules with satisfactory accuracy at comparably moderate cost. We apply these methods to study the photophysics and photochemistry of 4-(dimethyl)aminobenzonitrile (DMABN). DMABN is considered the paradigm of photoinduced intramolecular charge transfer (ICT), leading to dual fluorescence in polar solvents. By comparison of calculated emission energies, dipole moments, and vibrational frequencies with recent results from transient spectroscopy measurements, a definitive assignment of the electronic and geometric structure of the two lowest singlet excited states of DMABN is possible for the first time. We investigate the mechanism of the ICT reaction by means of minimum energy path calculations. The results confirm existing state-crossing models of dual fluorescence. Our study suggests that analytical TDDFT derivative methods will be useful to predict and classify emissive properties of other donor-acceptor systems as well.
Property-optimized Gaussian basis sets of split-valence, triple-zeta and quadruplezeta valence qu... more Property-optimized Gaussian basis sets of split-valence, triple-zeta and quadruplezeta valence quality are developed for the lanthanides Ce-Lu for use with small-core relativistic effective core potentials. They are constructed in a systematic fashion by augmenting def2 orbital basis sets with diffuse basis functions and minimizing negative static isotropic polarizabilities of lanthanide atoms with respect to basis set exponents within the unrestricted Hartree-Fock method. The basis set quality is assessed using a test set of 70 molecules containing the lanthanides in their common oxidation states and f electron occupations. 5d orbital occupation turns out to be the determining factor for the basis set convergence of polarizabilities in lanthanide atoms and the molecular test set. Therefore, two series of property-optimized basis sets are defined. The augmented def2-SVPD, def2-TZVPPD, and def2-QZVPPD basis sets balance the accuracy of polarizabilities across lanthanide oxidation states. The relative errors in atomic and molecular polarizability calculations are ≤ 8% for augmented split-valence basis sets, ≤ 2.5% for augmented triple-zeta valence basis sets, and ≤ 1% for augmented quadruple-zeta valence basis sets. In addition, extended def2-TZVPPDD and def2-QZVPPDD are provided for accurate calculations of lanthanide atoms and neutral clusters. The property-optimized basis sets developed in this work are shown to accurately reproduce electronic absorption spectra of a series of LnCp − 3 complexes (Cp = C 5 H 4 SiMe 3 , Ln = Ce-Nd, Sm) with timedependent density functional theory.
Angewandte Chemie, May 8, 2019
The nature of the processes at the origin of life that selected specific classes of molecules for... more The nature of the processes at the origin of life that selected specific classes of molecules for broad incorporation into cells is controversial. Among those classes selected were polyisoprenoids and their derivatives.T his paper tests the hypothesis that polyisoprenoids were early contributors to membranes in part because they (or their derivatives) could facilitate charge transport by quantum tunneling.I tm easures charge transport across self-assembled monolayers (SAMs) of carboxyl-terminated monoterpenoids (O 2 C(C 9 HX)) and alkanoates (O 2 C(C 7 HX)) with different degrees of unsaturation, supported on silver (Ag TS)b ottom electrodes,w ith Ga 2 O 3 / EGaIn top electrodes.M easurements of current density of SAMs of linear length-matched hydrocarbons-both saturated and unsaturated-showthat completely unsaturated molecules transport charge faster than those that are completely saturated by approximately afactor of ten. This increase in relative rates of charge transport correlates with the number of carboncarbon double bonds,b ut not with the extent of conjugation. These results suggest that polyisoprenoids-even fully unsaturated-are not sufficiently good tunneling conductors for their conductivity to have favored them as building blocks in the prebiotic world. Polyisoprenoids-also known as terpenoids-are ac lass of molecules found in all domains of life.A tt he cellular level, they serve both metabolic and structural roles. [1] Were polyisoprenoids selected for multiple functions (for example, the ability to conduct charge) at the beginning of life,o r purely for their availability and activity as surfactants? [2] Charge transport (CT) is important to anumber of biological
Enzyme Substrate Prediction from Three-Dimensional Feature Representations Using Space-Filling Curves
Journal of Chemical Information and Modeling, Feb 20, 2023
Journal of Physical Chemistry A, Mar 8, 2019
In this paper we develop a formal definition of chemical space as a discrete metric space of mole... more In this paper we develop a formal definition of chemical space as a discrete metric space of molecules and analyze its properties. To this end, we utilize the shortest path metric on reaction networks to define a distance function between molecules of the same stoichiometry (number of atoms). The distance between molecules with different stoichiometries is formalized by making use of the partial ordering of stoichiometries with respect to inclusion. Calculations of fractal dimension on metric spaces for individual stoichiometries show that they have low intrinsic dimensionality, about an order of magnitude less than the dimension of the underlying reactive potential energy surface. Our findings suggest that efficient search strategies on chemical space can be designed that take advantage of its metric structure.
Density functional methods have a long tradition in inorganic and bioinorganic chemistry. We intr... more Density functional methods have a long tradition in inorganic and bioinorganic chemistry. We introduce the density functional machinery and give an overview of most popular approximate exchange-correlation functionals. We present comparisons of density functionals for energies, structures, and reaction barriers of inorganic and bioinorganic systems, giving guidance on the title question. New development directions and current trends in density functional theory are reviewed.
Journal of Chemical Theory and Computation, Jun 4, 2019
Studying organic reaction mechanisms using quantum chemical methods requires from the researcher ... more Studying organic reaction mechanisms using quantum chemical methods requires from the researcher an extensive knowledge of both organic chemistry and first-principles computation. The need for empirical knowledge arises because any reasonably complete exploration of the potential energy surfaces (PES) of organic reactions is computationally prohibitive. We have previously introduced the Heuristically-Aided Quantum Chemistry (HAQC) approach to modeling complex chemical reactions, which abstracts the empirical knowledge in terms of chemical heuristics-simple rules guiding the PES exploration-and combines them with structure optimizations using quantum chemical methods. The HAQC approach makes use of heuristic kinetic criteria for selecting reaction paths that are not only plausible, that is, consistent with the empirical rules of organic reactivity, but also feasible under the reaction conditions. In this work, we develop heuristic kinetic feasilibity criteria, which correctly predict feasible reaction pathways for a wide range of simple polar (substitutions, additions, and eliminations) and pericyclic organic reactions (cyclizations, sigmatropic shifts, and cycloadditions). In contrast to knowledge-based reaction mechanism prediction methods, the same kinetic heuristics are successful in classifying reaction pathways as feasible or infeasible
Statistics and Bias-Free Sampling of Reaction Mechanisms from Reaction Network Models
Journal of Physical Chemistry A, Jun 7, 2023
Journal of the American Chemical Society, 2002
The electrical properties of self-assembled monolayers (SAMs) on metal surfaces have been explore... more The electrical properties of self-assembled monolayers (SAMs) on metal surfaces have been explored for a series of molecules to address the relation between the behavior of a molecule and its structure. We probed interfacial electron transfer processes, particularly those involving unoccupied states, of SAMs of thiolates or arylates on Au by using shear force-based scanning probe microscopy (SPM) combined with current-voltage (i-V) and current-distance (i-d) measurements. The i-V curves of hexadecanethiol in the low bias regime were symmetric around 0 V and the current increased exponentially with V at high bias voltage. Different than hexadecanethiol, reversible peak-shaped i-V characteristics were obtained for most of the nitro-based oligo(phenylene ethynylene) SAMs studied here, indicating that part of the conduction mechanism of these junctions involved resonance tunneling. These reversible peaked i-V curves, often described as a negative differential resistance (NDR) effect of the junction, can be used to define a threshold tip bias, VTH, for resonant conduction. We also found that for all of the SAMs studied here, the current decreased with increasing distance, d, between tip and substrate. The attenuation factor of hexadecanethiol was high, ranging from 1.3 to 1.4 Å-1 , and was nearly independent of the tip bias. The-values for nitro-based molecules were low and depended strongly on the tip bias, ranging from 0.15 Å-1 for tetranitro oligo(phenylene ethynylene) thiol, VII, to 0.50 Å-1 for dinitro oligo(phenylene) thiol, VI, at a-3.0 V tip bias. Both the VTH and values of these nitro-based SAMs were also strongly dependent on the structures of the molecules, e.g. the number of electroactive substituent groups on the central benzene, the molecular wire backbone, the anchoring linkage, and the headgroup. We also observed charge storage on nitro-based molecules. For a SAM of the dintro compound, V, ∼25% of charge collected in the negative scan is stored in the molecules and can be collected at positive voltages. A possible mechanism involving lateral electron hopping is proposed to explain this phenomenon.
Study of the Effect of Chromophore Environment on UV-Resonance Raman Scattering Spectroscopy of Tyrosine containing Short Peptides
To investigate changes in the resonance Raman in response to intermolecular interactions, we used... more To investigate changes in the resonance Raman in response to intermolecular interactions, we used an experimental and theoretical study of two series of peptides containing tyrosine and cysteine, and tyrosine and L-C-propargylglycine (PG), in solution, and in contact with the surface of titania anatase nanoparticles. Four technical barriers were shown in the course of this study. The first barrier was the incorrect assumption that high lying electronic states could be neglected. Our results show that for tyrosine, high energy electronic states out of resonance with the excitation can influence the Raman response and that intermolecular interactions can act on the molecular polarizability through these states. Three of the technical barriers were not overcome: 1) correct preparation of amino acid or peptide samples in close contact with the nanoparticle surfaces where signal predominantly arises from molecules on the surface, 2) correct calculation of peptides in contact with a trans...
Implementation of the self-consistent phonons method with ab initio potentials (AI-SCP)
The Journal of Chemical Physics
The self-consistent phonon (SCP) method allows one to include anharmonic effects when treating a ... more The self-consistent phonon (SCP) method allows one to include anharmonic effects when treating a many-body quantum system at thermal equilibrium. The system is then described by an effective temperature-dependent harmonic Hamiltonian, which can be used to estimate its various dynamic and static properties. In this paper, we combine SCP with ab initio (AI) potential energy evaluation in which case the numerical bottleneck of AI-SCP is the evaluation of Gaussian averages of the AI potential energy and its derivatives. These averages are computed efficiently by the quasi-Monte Carlo method utilizing low-discrepancy sequences leading to a fast convergence with respect to the number, S, of the AI energy evaluations. Moreover, a further substantial (an-order-of-magnitude) improvement in efficiency is achieved once a numerically cheap approximation of the AI potential is available. This is based on using a perturbation theory-like (the two-grid) approach in which it is the average of the d...
Selection bias is inevitable in manually curated computational reaction databases but can have a ... more Selection bias is inevitable in manually curated computational reaction databases but can have a significant impact on generalizability of quantum chemical methods and machine learning models derived from these data sets. We propose a new discrete representation of reaction mechanisms as subgraphs of a network of formal bond breaks and bond formations (transition network) composed of all shortest paths between reactant and product nodes. To construct a bias-free data set, the subgraphs between all pairs of network nodes (containing only neutral molecules) are considered. These quasireaction subgraphs include both reactive (reaction subgraphs) and non-reactive instances. The proposed approach thus transforms the problem of obtaining a bias-free data set of reaction mechanisms to binary classification of a set of quasireaction subgraphs that is free from selection bias by construction. We compute the statistics of the topological properties of quasireaction subgraphs in CHO reaction n...
In this paper we develop a formal definition of chemical space as a discrete metric space of mole... more In this paper we develop a formal definition of chemical space as a discrete metric space of molecules and analyze its properties. To this end, we utilize the shortest path metric on reaction networks to define a distance function between molecules of the same stoichiometry (number of atoms). The distance between molecules with different stoichiometries is formalized by making use of the partial ordering of stoichiometries with respect to inclusion. Calculations of fractal dimension on metric spaces for individual stoichiometries show that they have low intrinsic dimensionality, about an order of magnitude less than the dimension of the underlying reactive potential energy surface. Our findings suggest that efficient search strategies on chemical space can be designed that take advantage of its metric structure.<br>
arXiv (Cornell University), May 16, 2016
Recent work has shown that a fully many-body treatment of noncovalent interactions, such as that ... more Recent work has shown that a fully many-body treatment of noncovalent interactions, such as that given by the method of many-body dispersion (MBD), is vital to accurately modeling the structure and energetics of many molecular systems with density functional theory (DFT). To avoid double counting the correlation contributions of DFT and the MBD correction, a singleparameter range-separation scheme is typically employed. Coupling the MBD correction to a given exchange-correlation functional therefore requires calibrating the range-separation parameter. We perform this calibration for 24 popular DFT functionals by optimizing against the S66×8 benchmark set. Additionally, we report a linear equation that predicts near optimal range-separation parameters, dependent only on the class of the exchange functional and the value of the gradient enhancement factor. When a calibrated MBD correction is employed, most of the exchange-correlation functionals considered are capable of achieving agreement with CCSD(T)/CBS interaction energies in the S66×8 set to better than 1 kcal/mol mean absolute error.
arXiv (Cornell University), Aug 19, 2016
A fundamental problem in applying machine learning techniques for chemical problems is to find su... more A fundamental problem in applying machine learning techniques for chemical problems is to find suitable representations for molecular and crystal structures. While the structure representations based on atom connectivities are prevalent for molecules, two-dimensional descriptors are not suitable for describing molecular crystals. In this work, we introduce the SFC-M family of feature representations, which are based on Morton space-filling curves, as an alternative means of representing crystal structures. Latent Semantic Indexing (LSI) was employed in a novel setting to reduce sparsity of feature representations. The quality of the SFC-M representations were assessed by using them in combination with artificial neural networks to predict Density Functional Theory (DFT) single point, Ewald summed, lattice, and many-body dispersion energies of 839 organic molecular crystal unit cells from the Cambridge Structural Database that consist of the elements C, H, N, and O. Promising initial results suggest that the SFC-M representations merit further exploration to improve its ability to predict solid-state properties of organic crystal structures.
Libkrylov: A modular open-source software library for extremely large and dense eigenvalue and linear problems
Studying organic reaction mechanisms using quantum chemical methods requires from the researcher ... more Studying organic reaction mechanisms using quantum chemical methods requires from the researcher an extensive knowledge of both organic chemistry and first-principles computation. The need for empirical knowledge arises because any reasonably complete exploration of the potential energy surfaces (PES) of organic reactions is computationally prohibitive. We have previously introduced the Heuristically-Aided Quantum Chemistry (HAQC) approach to modeling complex chemical reactions, which abstracts the empirical knowledge in terms of chemical heuristics—simple rules guiding the PES exploration—and combines them with structure optimizations using quantum chemical methods. The HAQC approach makes use of heuristic kinetic criteria for selecting reaction paths that are not only plausible, that is, consistent with the empirical rules of organic reactivity, but also feasible under the reaction conditions. In this work, we develop heuristic kinetic feasilibity criteria, which correctly predict...
ACS Nano, 2018
Regulating energy transfer pathways through materials is a central goal of nanotechnology, as a g... more Regulating energy transfer pathways through materials is a central goal of nanotechnology, as a greater degree of control is crucial for developing sensing, spectroscopy, microscopy, and computing applications. Such control necessitates a toolbox of actuation methods that can direct energy transfer based on user input. Here we introduce a proposal for a molecular exciton gate, analogous to a traditional transistor, for regulating exciton flow in chromophoric systems. The gate may be activated with an input of light or an input flow of excitons. Our proposal relies on excitation migration via the second excited singlet (S 2) state of the gate molecule. It exhibits the following features, only a subset of which are present in previous exciton switching schemes: picosecond-timescale actuation, amplification/gain behavior, and a lack of molecular rearrangement. We demonstrate that the device can be used to produce 1 Page 1 of 32 ACS Paragon Plus Environment ACS Nano universal binary logic or amplification of an exciton current, providing an excitonic platform with several potential uses, including signal processing for microscopy and spectroscopy methods that implement tunable exciton flux.
Journal of chemical theory and computation, Jan 13, 2018
We report on the efficient turbomole implementation of quadratic response properties within the t... more We report on the efficient turbomole implementation of quadratic response properties within the time-dependent density functional theory (TDDFT) context that includes the static and dynamic dipole hyperpolarizability, ground-to-excited-state two-photon absorption amplitudes (through a single residue) and state-to-state one-photon absorption amplitudes (through a double residue). Our implementation makes full use of arbitrary (including non-Abelian) point-group symmetry as well as permutational symmetry and enables the calculation of nonlinear properties with hybrid density functionals for molecules with hundreds of atoms and thousands of basis functions at a cost that is a fixed multiple of the cost of the corresponding linear properties. Using the PBE0 hybrid density functional, we show that excited-state absorption spectra computed within the pseudowavefunction approach contain the qualitative features of transient absorption spectra tracking excimer formation in perylene diimide ...
The ability to regulate energy transfer pathways through materials is an important goal of nanote... more The ability to regulate energy transfer pathways through materials is an important goal of nanotechnology, as a greater degree of control is crucial for developing sensing, solar energy, and bioimaging applications. Such control necessitates a toolbox of actuation methods that can direct energy transfer based on user input. Here we propose a novel molecular exciton gate, analogous to a traditional transistor, for controlling exciton migration in chromophoric systems. The gate may be activated with an input of light or an input flow of excitons. Unlike previous gates and switches that control exciton transfer, our proposal does not require isomerization or molecular rearrangement, instead relying on excitation migration via the second singlet (S2) state of the gate molecule--hence the system is named an "S2 exciton gate." After presenting a set of system properties required for proper function of the S2 exciton gate, we show how one would overcome the two possible challenge...
Uploads
Papers by Dmitrij Rappoport